Scientific Publications
Associations between food production methods, antimicrobial resistance gene burden and diversity of microorganisms on retail food using metagenomics
Microbial Genomics
Food is produced by a range of methods including extensive (organic and free range) and intensive (conventional) production systems. Antimicrobial use varies between different food production systems, which may affect the microbial populations as well as the prevalence and diversity of antimicrobial resistance genes (ARGs) found on food at retail.
In this study metagenomics was used to investigate the microbial and ARG composition of 25 pork, 33 beef, 33 lamb, 60 chicken, 31 salmon, and 41 leafy-green samples collected in Norfolk, England, and labelled as extensive, wild caught, or intensive.
Food microbiomes consisted predominantly of spoilage-associated organisms including Pseudomonas, Lactococcus, and Psychrobacter. Significant differences in bacterial diversity were found between intensive and extensive systems on chicken, and 14 differentially abundant genera were identified between production systems across beef, chicken, and salmon. Genes conferring resistance to tetracyclines and beta-lactams comprised the majority of the food resistome across all commodities. No significant associations between individual ARG abundance, ARG diversity, nor the total concentration ARGs identified with qPCR, and production methods were observed. Our results suggest differently produced foods may not present an increased risk of antimicrobial resistance across the commodities investigated within this study. However, commodity specific associations were identified with the microbial composition across chicken, beef, and salmon. Additional work further up the processing chain is required to identify the drivers of these differences between production systems.
Microbial Genomics
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